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Objective: This research aimed to evaluate the effects of age on growth, tibia development, and intestinal calcium (Ca) and phosphorus (P) transporter gene expressions in broiler chickens.Methods: A total of 224 male Arbor Acres broilers were fed with nutrient-adequate diets and reared in eight cages (28 broilers per cage). Eight broilers (one broiler per cage) were selected and killed at 5, 10, 15, 20, 25, 30, 35, and 40 days of age, respectively.Results: Body weight continuously increased with age of broiler chickens from 5 to 40 days. The bone weight, ash weight, diameter, and length of the tibia also increased with broiler age. By contrast, the tibia ash, Ca, and P percentages quadratically changed with age (p

Carbon-fibre-reinforced structural Zn-ion battery composites achieved multifunctional performance with mechanically sturdy properties and high energy density.

Pancreatic ductal adenocarcinoma (PDAC) is considered ‘non-immunogenic’ with trials demonstrating its recalcitrance to PD1 and CTLA4 immune checkpoint therapies (ICTs). Here, we sought to systematically characterize the mechanisms underlying de novo ICT resistance and identify effective therapeutic options for PDAC. We report that agonist 41BB and antagonist LAG3 ICT alone and in combination, increased survival and anti-tumor immunity, characterized by modulating T cell subsets with anti-tumor activity, increased T cell clonality and diversification, decreased immunosuppressive myeloid cells and increased antigen presentation/decreased immunosuppressive capability of myeloid cells. Translational analyses confirmed the presence of 41BB and LAG3 in human PDAC. Since single and dual ICTs were not curative, T cell-activating ICTs were combined with a CXCR1/2 inhibitor, targeting immunosuppressive myeloid cells. Triple therapy resulted in durable complete responses. Given similar profiles in human PDAC and availability of these agents for clinical testing, our findings provide a testable hypothesis for this lethal disease.

Endometrial development is a complicated process involving numerous regulatory factors. Circular RNAs (circRNAs) have been known as a member of the naturally occurring non-coding RNA family, and are reportedly crucial for a variety of physiological processes. This study investigated the circRNA landscape of non-pregnant endometrium of dairy goats during estrus. Non-pregnant endometrial samples of goats at estrus day 5 (Ed5) and estrus day 15 (Ed15) were used to methodically analyze the circRNA landscape using strand-specific Ribo-Zero RNA-Seq. A total of 2 331 differentially expressed (P

Objective: Mutant KRAS is a primary driver of pancreatic ductal adenocarcinoma (PDAC), which exhibits marked hypoxia. Despite the strong association of hypoxia and PDAC, the relationship between KRAS and hypoxia is still poorly understood. The oxygen-sensitive histone lysine demethylase, KDM5A, was recently reported to mediate epigenetic responses to hypoxia independent of the hypoxia-inducible factors. KDM5A epigenetically represses transcription via two mechanisms: by its demethylase activity on activating H3K4me3 marks, and through its interaction with deacetylase complexes containing HDAC1/2, which deacetylates activating H3K9ac and H4K16ac histone marks. Under hypoxic conditions, KDM5A loses its activity, leading to restoration of these H3K4me3 marks, thereby activating KDM5A target genes. The purpose of this study is to understand how KDM5A loss of function contributes to pathogenesis of mutant KRAS-driven pancreatic cancer. Methods: Cell lines derived from mice with pancreas-specific p53 deletion and doxycycline-inducible expression of KrasG12D (iKPC). Protein lysates were prepared using RIPA buffer. Histones were purified by acid extraction. Immunoblotting was used to probe for protein levels of Kdm5a, H3K4me3, H3K9ac, and H4K16ac. Genetic ablation of KrasG12D was performed by culturing iKPCs in tetracycline-free medium. Kras was induced by adding doxycycline to the culture medium. Pharmaceutical inhibition of MEK, proteasome, and Kdm5a were performed by treating iKPCs with mirdametinib, MG-132, and CPI-455, respectively. Knockdown of β-TrCP and FBXW7 were performed by stable expression of shRNA in iKPCs. Protein motif scanning was performed using the Eukaryotic Linear Motif (ELM) Prediction online software. Results: We discovered that Kdm5a protein levels were abrogated by induction of KrasG12D and stabilized by genetic ablation of Kras. Pharmaceutical inhibition of MEK or proteasome function stabilized Kdm5a, indicating that Kras induces Kdm5a proteasomal degradation through the MEK/ERK pathway. H3K4me3, H3K9ac, and H4K16ac histone marks were increased in Kras-on iKPC compared to Kras-off iKPC, consistent the expected effect of Kras-induced Kdm5a degradation. Pharmaceutical inhibition Kdm5a in the Kras-off setting restored H3K4me3, suggesting that Kdm5a contributes to demethylation of H3K4me3 in iKPC. We identified two phosphodegron sites corresponding to β-TrCP and FBXW7 of the ubiquitin ligase complex within the Kdm5a protein sequence. Knockdown of either β-TrCP or FBXW7 in iKPC both stabilized Kdm5a despite induction of Kras. Conclusion: We conclude that Kdm5a plays a tumor suppressor role in pancreatic cancer by epigenetically repressing transcriptional programs necessary for KRAS-driven oncogenesis. Citation Format: Jasper R. Chen, Jincheng Han, Cullen M. Taniguchi, Ronald A. DePinho. Loss of KDM5A supports KRAS-driven pancreatic cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4757.

Exchangeable sodium can have pronounced influences on physicochemical soil properties whereas the combined impact on microbial turnover of organic carbon (OC) remains elusive. In this work, we aimed to differentiate the effects of exchangeable sodium and soil pH on microbially mediated aggregate formation and turnover of cattle slurry. We incubated the soils under controlled laboratory conditions using artificial soil model minerals containing quartz grains, montmorillonite and goethite. The montmorillonite was pre-treated with NaCl solutions of sodium adsorption ratios (SAR) 0, 1 and 5 which resulted in exchangeable sodium percentages (ESP) of 1, 7 and 19 on average. The soil pH was adjusted within two treatments to 7.5 and 8.5 for each ESP at the start of the incubation. We incubated these six treatments with and without cattle slurry ground to < 200 µm after addition of a combined microbial inoculum, extracted from a Cambisol (pHH2O 7.5, Germany) and a Calcaric Solonchak (pHH2O 9.3, Spain) added to all samples. The microcosms were incubated with three replicates over a period of 30 days at constant pF of 2.2. The CO2 emission measurements of the microcosms with exchangeable sodium indicated a delayed respiration. The respiration under ESP 19 increased rapidly within the first days of incubation, whereas it was more delayed under ESP 7 until 15 days of incubation. The delayed CO2 respiration might be related to inhibited structural formation in treatments with higher exchangeable sodium. To test this, we are investigating the data on water-stable aggregation by wet sieving. The delayed CO2 respiration was reflected in lower microbial biomass, extracted after the incubation. The microbial biomass under ESP 19 and pH 8.5 was highest whereas the amount of leached C after two rainfall events (at day 7 and 15) was lowest, which could be related to a higher microbially mediated OC sequestration. The composition of exchangeable cations was monitored before and after the whole incubation which might help explaining the processes of microbially mediated aggregate formation and microbial carbon turnover under different levels of exchangeable sodium.

BackgroundOptical coherence tomography (OCT) is an important modality used in coronary intervention. However, OCT requires a high amount of contrast media, limiting its extensive application in clinical practice. This study compared OCT images of coronary lesions obtained using contrast media and very-low contrast combined Ringer's solution (VLCCR) in patients with acute coronary syndrome (ACS).MethodsThirty ACS patients with a total of 36 native lesions and stenoses from 70 to 90% were included in this study. Two kinds of flushing media (a contrast medium and VLCCR) were used in succession in a random order for OCT image pullback of each lesion. VLCCR method is using low volume contrast (4–5 ml) injected into the guiding catheter previously combination with injector infused Ringer's solution instead of pure contrast medium. The safety of procedure was evaluated by recording the patients ‘symptoms, changes of ECG, blood pressure and heart rate. OCT images were analyzed to determine the image clarity. Lumen area and diameter were also measured and the consistency between the two media was compared.ResultsOCT procedure using either contrast or VLCCR did not show any peri-procedural adverse events. There was no difference in changes of blood pressure and heart rate in both procedures, however, VLCCR procedure showed less procedure-related symptoms and ECG changes. We found that the percentage of clear image frame was equivalent between the contrast and VLCCR media (98.0 vs. 96.9%, P = 0.90). We also observed a high degree of similarity between the different lesion phenotypes of ACS for both media. There was a linear correlation of the phenotypes obtained with these two different methods, and a significant correlation was observed between measurements obtained with contrast and VLCCR without correction for the refractive index of VLCCR (correlation coefficients ranged between 0.829 and 0.948).ConclusionsOCT imaging using VLCCR for blood clearance is feasible and safe and provides similar imaging quality compared to OCT imaging obtained using radiographic contrast media for ACS patients.

The growth of endometrial stromal cells (ESCs) at implantation sites may be a potential factor affecting the success rate of embryo implantation. Incremental proofs demonstrated that ncRNAs (e.g. miRNAs, lncRNAs and circRNAs) were involved in various biological procedures, including proliferation and apoptosis. In this study, the role of miR-100-5p on proliferation and apoptosis of goat ESCs in vitro and embryo implantation in vivo was determined. The mRNA expression of miR-100-5p was significantly inhibited in the receptive phase (RE) rather than in the pre-receptive phase (PE). Overexpression of miR-100-5p suppressed ESCs proliferation and induced apoptosis. The molecular target of MiR-100-5p, HOXA1, was confirmed by 3'-UTR assays. Meanwhile, the product of HOXA1 mRNA RT-PCR increased in the RE more than that in the PE. The HOXA1-siRNA exerted significant negative effects on growth arrest. Instead, incubation of ESCs with miR-100-5p inhibitor or overexpressed HOXA1 promoted the cell proliferation. In addition, Circ-9110 which acted as a sponge for miR-100-5p reversed the relevant biological effects of miR-100-5p. The intrinsic apoptosis pathway was suppressed in ESCs, revealing a crosstalk between Circ-9110/miR-100-5p/HOXA1 axis, PI3K/AKT/mTOR, and ERK1/2 pathways. To further evaluate the progress in study on embryo implantation regulating mechanism of miR-100-5p in vivo, the pinopodes of two phases were observed and analysed, suggesting that, as similar as in situ, miR-100-5p was involved in significantly regulating embryo implantation in vivo. Mechanistically, miR-100-5p performed its embryo implantation function through regulation of PI3K/AKT/mTOR and ERK1/2 pathways by targeting Circ-9110/miR-100-5p/HOXA1 axis in vivo.

ArsR-family transcriptional factors regulates diverse physiological functions necessary for Brucella adaptation to environmental changes. However, whether the ArsR-family transcriptional regulator are related to virulence, and the precise determination of ArsR direct targets in Brucella are still unknown. Therefore, we created a 2308ΔArsR6 mutant of B. abortus 2308 (S2308). Virulence assay was performed using a murine macrophage cell line (RAW 264.7). We performed chromatin immunoprecipitation of ArsR6 followed by next-generation sequencing (ChIP-seq). We also selected the target gene pobA (BAB2_0600), and created the mutant (2308ΔpobA). The survival capability of 2308ΔpobA strain in RAW 264.7 was detected and the levels of tumor necrosis factor-α (TNF-α), interferon-gamma (IFN-γ), interleukin-12 (IL-12) and interleukin-18 (IL-18) were also measured. The results showed that 2308ΔArsR6 reduced survival capability in RAW 264.7. We detected 40 intergenic ChIP-seq peaks of ArsR6 binding distributed across the Brucella genome. 2308ΔpobA was significantly reduced survival capability in RAW 264.7. After the macrophages were infected with 2308ΔpobA, the levels of TNF-α, IFN-γ, IL-12 and IL-18 were decreased and were significantly lower than that for the S2308-infected group, indicating that the 2308ΔpobA could reduce the secretion of inflammatory cytokines. Taken together, the research provided new insights into the functionality of ArsR6 and great significance to clarify the function of ArsR6.

A crude oil spill in 2014 resulted in extensive soil contamination of the hyper arid Evrona Nature Reserve in Israel’s Negev Desert. The contaminated soils became highly hydrophobic, threatening the existence of plants in the habitat. We hypothesized that bioaugmenting the soil with indigenous biosurfactant-producing, hydrocarbon-degrading bacteria (HDB) would accelerate the reduction in the soil’s hydrophobicity. We aimed to isolate and characterize biosurfactant-producing HDBs from the desert-contaminated soil and test if they can be used for augmenting the soil. Twelve hydrocarbon-degrading strains were isolated, identified as Pseudomonas, and classified as biosurfactants “producing” and “nonproducing”. Inoculating 109 CFU/g of “producing” strains into the polluted soil resulted in a 99.2% reduction in soil hydrophobicity within seven days. At the same time, nonproducing strains reduced hydrophobicity by only 17%, while no change was observed in the untreated control. The microbial community in the inoculated soil was dominated by the introduced strains over 28 days, pointing to their persistence. Rhamnolipid biosynthesis gene rhlAB remained persistent in soil inoculated with biosurfactants, indicating in situ production. We propose that the success of the treatment is due to the use of inoculum enriched from the polluted soil.

Autumn fertilization is an important cultivation and management measure used to provide nutrients at the hardening stage during the end of the growing season-bolstering nutrient reserves and promoting additional growth in the following spring. Previous studies mainly focused on short-term or one-time fertilization treatment of container seedlings, and few studies have observed the effects of autumn fertilization of large-area forests over multiple continuous years. The growth dynamics and nutrient changes during autumn in 324

Transcriptomics is an established powerful tool to identify potential mRNAs and ncRNAs (non‐coding RNAs) for endometrial receptivity. In this study, the goat endometrium at estrus day 5 (ED5) and estrus day 15 (ED15) were selected to systematically analyse the differential expressed genes (DEGs) what were induced by the embryo. There were 1,847 genes which were significantly differential expressed in endometrium induced by the embryo at ED5, and 1,346 at ED15 (p‐value, In this study, the goat endometrium at estrus day 5 and estrus day 15 were selected to systematically analyse the DEGs induced by the embryo in the endometrium of dairy goats, and there were 1,847 genes that were differential expressed at ED5, and 1,346 at ED15. In a word, this resulting view of the transcriptome greatly uncovered the global trends in mRNAs expression induced by the embryo in the endometrium of dairy goats.

Carbon fiber-reinforced polymer (CFRP) composites have excellent structural properties and potential multifunctionality, but thermal conductivity enhancement is desired to meet the heat transfer requirement due to low thermal conductivity in the through-thickness direction. The micro-nano boron nitride (BN) fillers were incorporated into the CFRP by the acetone vehicle-solvent to prepare three phase composites with relatively high thermal conductivity. Three prediction models were presented to estimate the thermal conductivity of composites respectively based on component configurational correlation, filler penetration degree, and ease of conductive chains formation. Most predicted results for modified composites show good agreement with experiments. The effects of vehicle-solvent concentration on microsurface morphology of prepreg and thermal conductivity of composites were conducted, and the thermal modification mechanism was explored based on above-mentioned and filler distribution. The tensile responses of modified composites also show obvious difference as the variation of vehicle-solvent concentration. The degradation of mechanical property suggests that it is a couple of potential challenges between structural property and thermal functionality.

The application of single-cell RNA sequencing platforms has generated notable insights into the heterogeneity underlying pancreatic ductal adenocarcinoma (PDAC), encompassing both the neoplastic compartment and the tumour microenvironment. In this Comment, we discuss the most pertinent findings gleaned from both mouse models and human PDAC samples, as well as future opportunities.

Carbon distribution in plants and ecological stoichiometry in soils are important indicators of element cycling and ecosystem stability. In this study, five forest ages, young forest (YF), middle-aged forest (MAF), near-mature forest (NMF), mature forest (MF), and over-mature forest (OMF) in a Pinus tabuliformis plantation were chosen to illustrate interactions among the C: N: P stoichiometry in soils and carbon distribution in plants, in the mountainous area of eastern Liaoning, China. Carbon content was highest in the leaves of MAF (505.90 g⋅kg−1) and NMF (509.00 g⋅kg−1) and the trunks of YF (503.72 g⋅kg−1), MF (509.73 g⋅kg−1), and OMF (504.90 g⋅kg−1), and was lowest in the branches over the entire life cycle of the aboveground components (335.00 g⋅kg−1). The carbon content of the fine roots decreased with soil layer depth. In YF, MAF, and NMF carbon content of fine roots at 0.5 m was always higher than that of fine roots at 1 m; however, it was the opposite in MF and OMF. The carbon content of the leaves changed with forest age; however, carbon content of branches, trunks and fine roots did not change significantly. Soil total carbon (TC), total nitrogen (TN), total phosphorus (TP), and available phosphorus (AP) content was highest in the OMF. Soil TC, TN and AP content, and TC: TN, TC: TP and TN: TP ratio decreased with increasing soil depth. Soil TC, TN, and TP content had a significant effect on the carbon content of fine roots (p < 0.05). The leaf carbon content and soil element content changed obviously with forest age, and the soil TN, TP and AP increased, which might reduce the carbon content allocation of fine roots.

Additional file 1: Fig. S1. Methodology of the framework. a. Illustration of minimal event distance (MED) calculation. b. Average lineage partitioning accuracy (LPA) on 100 simulation datasets without noise. c. Estimating lineage specific cumulative fold level (CFL). d. Estimating significance of CFL in an individual sample. e. AUC of non-random fitness-associated alterations (FAAs) detection based on LSA, permutated SCCN matrix rather than reconstructing tree, GISTIC test and one-side Wilcoxon signed-rank test on 100 simulation datasets without noise. f. Identification of non-random fitness-associated CNAs in a cohort of samples. g. Identification of parallel evolution CNAs in an individual sample. Fig. S2. The efficiency of MEDALT based on 9 × 3 × 20 simulation datasets with the population size from 400 to 2000, genome size from 100 to 1000. Fig. S3. Simulation and evaluation of CNA evolution model. a. Illustration of simulated genomic structural rearrangements in the evolution of a tumor. K represents the number of CNAs during ∆t period. r represents the number of adjacent regions which are affected by a CNA. TD: tandem duplication. TER: terminal deletion. DEL: interstitial deletion. BFB: breakage fusion bridge. b. Simulated and inferred copy number evolution distance between two genomes. Compared with MED are commonly used distance metrics Hamming, Euclidean and Manhattan. c. The AUC for identifying FAAs based on different combinations of models. Wilcox represents one-side Wilcoxon signed-rank test. d. The effects of noise on FAAs detection. Fig. S4. SCCN profile of TNBC patient KTN102. Each row represents a cell from pre-, mid-, or post-treatment. Fig. S5. Average distance between root node and cells from pre-, mid- or post-treatment based on MEDALT, maximal parsimony (MP), neighbor-joining (NJ) and maximum likelihood tree. FC refers to the fold changes between the average distance to root of the mid−/post- cells and that of the pre-treatment cells. Fig. S6. Stratified average CNA rates and fractions of DDR genes loss among lineages (distinguished by colors) in 6 primary TNBC samples. Fig. S7. Gene set enrichment analysis (GSEA) for genes identified by LSA in patient t1. Colors correspond to branches. Fig. S8. Significant genes identified through cohort LSA from the TNBC scDNA-seq data. a. Venn diagram of the genes identified by the MEDALT, MP and GISTIC but not reported in oncoKB, COSMIC and intOGen. b. Overall survival (OS) analysis of breast cancer patients in TCGA. c. Progression free survival (PFS) analysis of breast cancer patients in TCGA. d. Overall survival analysis of breast cancer patients in the METABRIC. e. The fraction of cancer genes overlapping with events which were significant in single lineage (#Lineage = 1), multiple lineages (#Lineage > 1), parallel evolution test ((#Lineage > 1& PLSA

Additional file 6.

Additional file 7. Review history.

The present study aims to compare the relative bioavailability (RBV) of 1α-hydroxycholecalciferol (1α-OH-D3) to cholecalciferol (D3) in 1- to 21-d-old broiler chicks fed with calcium (Ca)- and phosphorus (P)-deficient diets. A total of 400 male of 1-d-old Ross 308 broilers were randomly assigned to 8 treatments with 5 replicates each. Five levels of D3 (0, 2.5, 5, 10, and 20 µg/kg) and three levels of 1α-OH-D3 (1.25, 2.5, and 5 µg/kg) were added to a basal diet. The basal diet contained 0.50% Ca and 0.25% non-phytate phosphorus (NPP), without D3. The RBV of 1α-OHD3 to D3 was determined by the slope ratio method. Using bodyweight gain, feed intake, feed efficiency, and plasma Ca as criteria, the RBV of 1α-OH-D3 to D3 were 4.78, 4.75, 4.50, and 4.21, respectively. Using tibia breaking-strength, weight, length, width, ash weight and content, and Ca and P content as criteria, the RBV of 1α-OH-D3 to D3 were 5.58, 5.16, 4.42, 4.70, 5.03, 4.46, 4.70, and 4.79. Using femur weight, length, width, ash weight and content, and Ca and P content as criteria, the RBV of 1α-OH-D3 to D3 were 5.09, 4.43, 3.19, 5.83, 5.21, 5.27, and 5.31. Using metatarsus weight, length, width, ash weight and content, and Ca and P content as criteria, the RBV of 1α-OHD3 to D3 were 5.00, 4.05, 5.94, 4.73, 5.33, 5.64, and 4.28. These data indicate that the RBV of 1α-OH-D3 to D3 is 4.84 in promoting growth performance and bone mineralization in broilers from 1 to 21 d of age.

This protocol describes two innovative algorithms: 1) A minimal event distance aneuploidy lineage tree (MEDALT) inference algorithm allows implementing genetically meaningful distances and is scalable to current single-cell datasets containing thousands of cells, and 2) A statistical routine, Lineage Speciation Analysis (LSA), enables prioritization of CNAs and genes that are non-randomly associated with the observed lineage expansion and thereby are potentially functionally important.

Aneuploidy plays critical roles in genome evolution.Alleles, whose dosages affect the fitness of an ancestor, will have altered frequencies in the descendant populations upon perturbation.Single-cell sequencing enables comprehensive genome-wide copy number profiling of thousands of cells at various evolutionary stage and lineage. That makes it possible to discover dosage effects invisible at tissue level, provided that the cell lineages can be accurately reconstructed.Here, we present a Minimal Event Distance Aneuploidy Lineage Tree (MEDALT) algorithm that infers the evolution history of a cell population based on single-cell copy number (SCCN) profiles. We also present a statistical routine named lineage speciation analysis (LSA), which facilitates discovery of fitness-associated alterations and genes from SCCN lineage trees.We assessed our approaches using a variety of single-cell datasets. Overall, MEDALT appeared more accurate than phylogenetics approaches in reconstructing copy number lineage. From the single-cell DNA-sequencing data of 20 triple-negative breast cancer patients, our approaches effectively prioritized genes that are essential for breast cancer cell fitness and are predictive of patient survival, including those implicating convergent evolution. Similar benefits were observed when applying our approaches on single-cell RNA sequencing data obtained from cancer patients.The source code of our study is available at https://github.com/KChen-lab/MEDALT.

Gut microbiota has been demonstrated to play multiple crucial roles in immunity, physiology, metabolism, and health maintenance. Diarrhea was closely related to the gut microbiota, but information regarding the alterations in gut microbial composition and structure in Baer's Pochard (Aythya baeri) with diarrhea remains scarce. Here, 16S rDNA amplicon sequencing was performed to investigate the gut microbial variability between diarrheic and healthy Baer's Pochard. Results indicated that the gut bacterial community of diarrheic Baer's Pochard showed a distinct decrease in alpha diversity, accompanied by evident changes in taxonomic compositions. Microbial taxonomic analysis revealed that Firmicutes, Proteobacteria and Bacteroidetes were the most dominant phyla in all the fecal samples regardless of health status. At the genus level, the differences in gut bacterial abundance between healthy and diarrheic populations were gradually observed. Specifically, the proportion of Elusimicrobia in the diarrheic Baer's Pochard was increased in comparison with healthy populations, while Acidobacteria, Rokubacteria, Cyanobacteria and Patescibacteria were dramatically decreased. Additionally, the relative proportion of 23 bacterial genera significantly decreased in diarrheic Baer's Pochard, whereas the relative percentage of 4 bacterial genera (Alkanindiges, Elusimicrobium, Spirosoma and Exiguobacterium) observably increased as compared to healthy populations. Taken together, the present study revealed that there were distinct differences in the gut microbial composition and diversity between the healthy and diarrheic Baer's Pochard. Remarkably, this is the first report on the differences in the gut microbiota of Baer's Pochard under different health states and may contribute to provide better insight into gut microbial composition and diversity of Baer's Pochard.

It is essential to improve animal vaccine for brucellosis since conventional vaccines are residual virulent and poor protective effect, limit their applications. To solve these problems, the recombinant DNA vaccines were appeared, which could improve protective immunity and were attenuated to animals. In current research, the recombinant DNA vaccine (pVGntR) based on transcriptional regulator GntR of Brucella abortus (B. abortus) was constructed. The results show that pVGntR is significantly more protective than the conventional RB51 vaccine. Immunization with pVGntR increases the production of immunoglobulin G (IgG) and elicits elevated numbers of gamma interferon (IFN-γ) and interleukin-4 (IL-4). These results suggest that pVGntR is a highly efficacious vaccine candidate that confers protection against wild-type B. abortus challenge.

microRNAs (miRNAs) and circular RNAs (circRNAs) are important for endometrial receptivity establishment and embryo implantation in mammals. miR-34a and miR-34c are highly expressed in caprine receptive endometrium (RE). Herein, the functions and mechanisms of miR-34a/c in caprine endometrial epithelial cell (CEEC) apoptosis and RE establishment were investigated. miR-34a/c downregulated the expression level of centrosomal protein 55 (CEP55) and were sponged by circRNA8073 (circ-8073), thereby exhibiting a negative interaction in CEEC. miR-34a/c induced CEEC apoptosis by targeting circ-8073/CEP55 through the regulation of the RAS/RAF/MEK/ERK and phosphoitide 3-kinase (PI3K)/protein kinase B (AKT)/mammalian target of rapamycin (mTOR) pathways. Positive and negative feedback loops and cross-talk were documented between the RAS/RAF/MEK/ERK and PI3K/AKT/mTOR pathways. miR-34a/c regulated the levels of RE marker genes, including forkhead box M1, vascular endothelial growth factor, and osteopontin (OPN). These results suggest that miR-34a/c not only induce CEEC apoptosis by binding to circ-8073 and CEP55 via the RAS/RAF/MEK/ERK and PI3K/AKT/mTOR pathways, but may also regulate RE establishment in dairy goats.

Previous observations from in-situ biological treatments in the subsurface of a perchlorate-contaminated site revealed multiple reduction processes occurring parallel to perchlorate degradation. Iron reduction was accelerated and correlated with a decline in the efficiency of the in-situ perchlorate reduction. In the current study, we examined the influence of iron forms on perchlorate reduction. A series of kinetic laboratory experiments were conducted, using an indigenous mixed perchlorate-reducing culture, enriched from the polluted soil that was undergoing bioremediation. The results show that ferrous iron was a non-competitive inhibitor with a 41% decrease in µmax for perchlorate reduction. Moreover, chlorate was accumulated in all samples treated with ferrous iron, indicating a disruption to the chlorate reduction step. Ferric iron, however, had less impact on perchlorate degradation with non-competitive inhibition reaching a 23% decrease in µmax. Scanning electron microscopy (SEM) revealed that the presence of ferrous iron in the perchlorate degradation enrichment culture initiated cell encrustation. We propose that during perchlorate reduction and the emission of oxygen from chlorite dismutation, the chemical oxidation of ferrous iron occurred near the bacteria's surface where the enzyme is located, forming an oxidized iron crust layer that can directly affect the perchlorate reduction enzymatic system.

Cancer stem cells (CSCs) are self-renewing cells that facilitate tumor initiation, promote metastasis, and enhance cancer therapy resistance. Transcriptomic analyses across many cancer types have revealed a prominent association between stemness and immune signatures, potentially implying a biological interaction between such hallmark features of cancer. Emerging experimental evidence has substantiated the influence of CSCs on immune cells, including tumor-associated macrophages, myeloid-derived suppressor cells, and T cells, in the tumor microenvironment and, reciprocally, the importance of such immune cells in sustaining CSC stemness and its survival niche. This review covers the cellular and molecular mechanisms underlying the symbiotic interactions between CSCs and immune cells and how such heterotypic signaling maintains a tumor-promoting ecosystem and informs therapeutic strategies intercepting this co-dependency.

Aneuploidy, the phenomenon that genomes acquire or lose chromosomal fragments, has been causally implicated in a wide variety of human cancer. Defining which copy number alterations (CNAs) are pathogenic is an important goal of cancer research. However, data based on bulk samples cannot fully depict tumor heterogeneity and evolution, which occurs in single cells, and thus have limited power to discover CNAs useful for cancer diagnostics and therapeutics. Recent advances in single-cell DNA sequencing have enabled acquisition of single-cell copy number (SCCN) profiles in tens of thousands of cells, which potentiate reconstruction of copy number evolution lineage and discovery of novel cancer genes. However, current analytical approaches that infer clonal lineages are neither accurate, nor scalable to analyzing molecular features, particularly CNA profiles obtained from thousands of cells. Statistical routines have not been established to leverage lineage tracing results towards identifying cancer-related genes. Here, we present a Minimal Event Distance Aneuploidy Lineage Tree (MEDALT) algorithm that infers the evolution history of a cell population based on single-cell copy number (SCCN) profiles. In a MEDALT, each node represents a cell, each edge represents a kinship between two cells, arrows point towards younger cells, and the root represents a normal diploid cell. We also present a statistical routine named lineage speciation analysis, which facilitates discovery of fitness-associated alterations (FAAs) and genes from SCCN lineage trees. To evaluate MEDALT, we simulated copy number evolution under various CNA mechanisms such as genome doubling, breakage-fusion-bridge (BFB), etc. and spiked in FAAs. We found that MEDALT substantially improved accuracy of FAA identification over GISTIC and conventional phylogenetics methods such as maximum likelihood (ML), maximal parsimony (MP) and neighbor joining (NJ) trees. We applied our methods on the single-cell DNA-sequencing data acquired from 20 triple-negative breast cancer patients (TNBCs), 4 of which had longitudinal pre-, mid- and post- treatment samples. Most of the TNBC samples appeared to have developed through branched evolution via multiple parallel lineages with distinct mutation rates and DNA damage repair (DDR) loss based on the constructed MEDALT. Using our approaches, we discovered novel genes that are predictive of patient survival in TCGA breast cancer data and are functionally more essential than other control gene sets, based on the CRISPR-cas9 knockout screen data obtained from 27 breast cancer cell lines in the DepMap database. Significant benefits in lineage tracing and cancer gene discovery were also achieved, when applying our approaches on the SCCN profiles derived using InferCNV from the single-cell RNA sequencing data of a cohort of 20 multiple myeloma, head and neck cancer, oral squamous cell carcinoma and ovarian cancer patients. The source code of our study is available at https://github.com/KChen-lab/MEDALT. Citation Format: Fang Wang, Qihan Wang, Vakul Mohanty, Shaoheng Liang, Jinzhuang Dou, Jincheng Han, Darlan Minussi, Ruli Gao, Li Ding, Nicholas Navin, Ken Chen. Single-cell copy number heterogeneity tracing enabling cancer gene discovery [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PO-017.

Copy number alterations (CNAs) play an important role in cancer development and treatment. CNA profiles in single tumor cells preserve archaeological records of a tumor evolution, enabling retrospective lineage tracing. Although current single-cell sequencing technologies have enabled accurate, high-throughput acquisition of single-cell integer CNA profiles, existing computational methods are neither intelligent, i.e., unaware of CNA evolution mechanisms such as breakage-fusion-bridge, nor scalable to current datasets consisting of thousands of cells. To address this challenge, we developed a novel, efficient computational approach, Medatree (minimal event distance aneuploidy tree) to infer a cell lineage tree from the whole genome CNA profiles of a large number (N>1,000) of cells obtained from patient samples. A tree inferred by Medatree describes the minimal number of single-copy gain or loss events that may have occurred during the evolution, the genealogical relations amongst individual cells, and the significant CNAs associated with lineage expansion. We confirmed through simulation that Medatree substantially improves lineage tracing accuracy (e.g., 0.73 vs. 0.31) over conventional phylogeny methods (e.g., maximum parsimony). We then applied Medatree to single-cell DNA sequencing (scDNA-seq) data obtained from 20 triple-negative breast cancer patients (TNBCs), some of which had longitudinal biopsies through the course of chemotherapy. The trees constructed by Medatree corroborated well with the timing and phenotypes of the biopsies. They also revealed branches with variable CNA rates, likely associated with differentially altered genome instability. We further identified significantly copy-number altered genes through permutation of the single-cell CNA profiles. Compared to results obtained by applying convention methods (phylogenetic trees and GISTIC) on the same datasets, Medatree detected more genes (1.6-fold) that have been functionally associated with breast cancer development and treatment outcome, proving the power of single-cell sequencing. Moreover, it revealed potential convergent CNA (such as gain of IGF1R) occurring in parallel lineages of a tumor sample in 3 out of 20 TNBCs. Similar gains in discovery power were observed when applying Medatree on CNA profiles derived from single-cell RNA sequencing (scRNA-seq) data of 12 multiple myeloma patients. In summary, we developed a first-of-its-kind approach Medatree that enables large-scale retrospective CNA lineage tracing from single-cell copy number profiles obtained from single-cell DNA and RNA-sequencing data of patient samples. Wide application of Medatree is expected to accelerate the study of copy number evolution during tumor development and lead to discovery of novel targets for diagnoses and treatments. The source code of Medatree is available at https://github.com/KChen-lab/Medatree. Citation Format: Fang Wang, Qihan Wang, Jincheng Han, Vakul Mohanty, Shaoheng Liang, Darlan Conterno Minussi, Ruli Gao, Li Ding, Nicholas Navin, Ken Chen. Medatree enabling single cell copy number lineage tracing and functional discovery [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4424.

An Experimental investigation was conducted to compare the evaporation characteristics of R410A inside three newly developed horizontal enhanced heat transfer (EHT) tubes with the same OD12.70mm and ID11.50mm, and the result of them are compared with that of a plain tube. The inner enhanced surface of 1EHT tube consists of dimples/protrusions and petal arrays, while that of 2EHT-1 tube and 2EHT-2 tube is composed by longitudinal grooves and dimples of different depths. The mass velocities are in the range of 70kg/m2s-200kg/m2 s with a nominal saturation temperature fixed at 279K and the vapor quality in the test section varies from 0.2∼0.9. As the mass flux increases, both the heat transfer coefficient and pressure penalty increase accordingly. The heat transfer coefficient of EHT tubes can achieve 1.14–1.53 times higher than that of the smooth tube while the pressure gradients is 1.43–1.83 times larger than that of smooth tubes. Besides, the enhancement ratios of all the enhanced surface tubes are larger than their respective surface area ratio, and the enhancement ratio comparisons of heat transfer coefficient are made to obtain the enhancing mechanism. The results show that the EHT tubes appear higher performance at low mass fluxes. In all, the EHT1 tube has the best heat transfer performance at low mass velocity, which can be attributed to its special enhanced inner surface, resulting in the increase of nucleation sites, flow separation and turbulent fluctuations. The other two 2EHT tubes can enhance the evaporation greatly with small respective surface ratios as well as relatively little pressure drop penalty, and them shows outstanding performance especially at high mass velocity.

The profiling of abnormally-expressed proteins in host cells using mass spectrometry (MS) analysis is a classical approach for screening disease-associated biomarkers in clinical diagnosis. However, few pathogen-specific antigens can currently be detected in serum using this proteomic approach, since these are very low-abundant proteins that are easily masked by host high-abundant proteins. Identification of pathogen-specific antigens in the sera of tuberculosis patients is crucial for the clinical diagnosis of this infectious disease, especially in immune-compromised patients. In the present study, two biomimetic affinity chromatography (BiAC) media, At-23 and A115-94, were selected from a library of BiAC media and used to selectively fractionate Albumin and Immunoglobulin from sera, respectively, prior to MS analyses. Each fraction was collected and screened against the proteomic database of M. tuberculosis complex. Three antigens, FbpA, FbpB and BfrB, were identified with two distinct peptides in BiAC-fractionated sera from tuberculosis patients, which were confirmed by Western blotting. Moreover, the identification of pathogen-specific antigens in sera by BiAC in conjunction with ESI-CID-MS/MS represents a promising strategy for the discovery of disease-associated biomarkers in other diseases.

Uterine receptivity for the embryo is established and maintained through a series of precise cellular and molecular events, such as DNA methylation. There have been no studies to elucidate entire genome DNA methylation changes associated with embryo receptivity development of the endometrium (RE). In the present study, there was development of a complete genome-wide DNA methylome maps of the RE using whole-genome bisulphite sequencing and bioinformatics analysis. As many as 163.06 Gb of sequencing data averaging 81.53 Gb per sample were obtained for genome bisulphite sequencing of endometrium samples. There were distinct genome-wide DNA methylation patterns in pre-receptive endometrium (PE; Day 5 of gestation) and RE (Day 15 of gestation). There were as many as 16,467 differentially methylated regions (DMRs); 21,391 DMRs were less methylated in RE samples compared with PE samples (P-values ≤ 0.05 and |log2 (fold change)| ≥ 2). Compared with PE samples, methylation ratios of IGF2BP2, ACOX2, PTGDS, VEGFB and PTGDR2 genes were markedly less in RE samples (P-value ≤ 0.05 and |log2 (fold change)| ≥ 2). Conversely, in RE samples there was a markedly greater methylation ratio of IGFBP3 and IGF1R genes. The results of KEGG analysis indicated that these genes were involved in the signalling pathways for insulin, mitogen-activated protein kinase, gonadotropin-releasing hormone, vascular endothelial growth factor and progesterone-mediated oocyte maturation, which participated in differential regulation of goat endometrial development during receptive and prereceptive phases. The results of previous and the present study indicate resulting proteins of IGF2BP2, PTGDS, VEGFB, PGR, IGFBP3 and IGF1R gene expression may have important functions in regulating endometrial receptivity for the embryo.

Bacterial homologous chloroplast-targeted Obg GTPases (ObgCs) belong to the plant-typical Obg group, which is involved in diverse physiological processes during chloroplast development. However, the evolutionarily conserved function of ObgC in plants remains elusive and requires further investigation. In this study, we identified DoObgC from an epiphytic plant Dendrobium officinale and demonstrated the characteristics of DoObgC. Sequence analysis indicated that DoObgC is highly conserved with other plant ObgCs, which contain the chloroplast transit peptide (cTP), Obg fold, G domain, and OCT regions. The C terminus of DoObgC lacking the chloroplast-targeting cTP region, DoObgCΔ1-160, showed strong similarity to ObgE and other bacterial Obgs. Overexpression of DoObgCΔ1-160 in Escherichia coli caused slow cell growth and an increased number of elongated cells. This phenotype was consistent with the phenotype of cells overexpressing ObgE. Furthermore, the expression of recombinant DoObgCΔ1-160 enhanced the cell persistence of E. coli to streptomycin. Results of transient expression assays revealed that DoObgC was localized to chloroplasts. Moreover, we demonstrated that DoObgC could rescue the embryotic lethal phenotype of the Arabidopsis obgc-t mutant, suggesting that DoObgC is a functional homolog to Arabidopsis AtObgC in D. officinale. Gene expression profiles showed that DoObgC was expressed in leaf-specific and light-dependent patterns and that DoObgC responded to wounding treatments. Our previous and present studies reveal that ObgC has an evolutionarily conserved role in ribosome biogenesis to adapt chloroplast development to the environment.

Brucellosis is an important zoonotic disease of worldwide distribution, which causes animal and human disease. However, the current Brucella abortus (B. abortus) vaccines (S19 and RB51) have several drawbacks, including residual virulence for animals and humans. Moreover, S19 cannot allow serological differentiation between infected and vaccinated animals. We constructed double deletion (ΔNodVΔNodW) mutant from virulent B. abortus 2308 (S2308) by deleting the genes encoding two-component regulatory system (TCS) in chromosome II in S2308.2308ΔNodVΔNodW was significantly reduced survival in murine macrophages (RAW 264.7) and BALB/c mice. Moreover, the inoculated mice showed no splenomegaly. The mutant induced high protective immunity in BALB/c mice against challenge with S2308, and elicited an anti-Brucella-specific immunoglobulin G (IgG) response and induced the secretion of gamma interferon (IFN-γ) and interleukin-4 (IL-4). Moreover, NODV and NODW antigens would allow the serological differentiation between infected and vaccinated animals. These results suggest that 2308ΔNodVΔNodW mutant is a potential live attenuated vaccine candidate and can be used effectively against bovine brucellosis.

Iron is often found to be of excessive concentrations in laying hens' diets, which may cause antagonistic interactions with other minerals. This study was conducted to investigate how to supplement Zn and Mn in the diets without Fe supplementation. In experiment 1, 420 18-week Lohmann Brown layers were fed a basal diet or a basal diet supplemented with 30-0, 65-30 and 100-60 mg/kg of Zn and Mn, respectively. In experiment 2, 360 40-week Lohmann Brown layers were fed a basal diet or a basal diet supplemented with 15-0, 35-0 and 55-15 mg/kg of Mn and Zn, respectively. Minerals were supplemented in the form of sulfate. Egg production was improved by supplementing 30 mg/kg Zn or 65 mg/kg Zn in combination with 30 mg/kg Mn in experiment one. In experiment two, a significant reduction of egg performance occurred with 35 mg/kg Mn supplementation. Mn and/or Zn supplementation increased eggshell thickness in experiment one, and decreased yolk cholesterol in both experiments. Mn and/or Zn supplementation increased Zn and Mn excretion in both experiments. Serum growth hormone (GH), thyroxine (T(4) ), and insulin levels, or alkaline phosphatase (AP) activity were not affected by treatments; serum estrogen (E(2) ) and triiodothyronine (T(3) ) were different but there was no consistency by dietary treatments. This study demonstrates that 30 mg/kg supplemental Zn is necessary to obtain maximal egg production, and there seems to be no need to supply Mn in this type of diet.

A trial was conducted to study the influence of different levels of a commercial enzyme complex on performance, nutrient availability, blood parameters, digestive tract measurements, amylase and trypsin activity of the digestive tract and gut morphology in broilers fed the typical diets in north China. There were four treatments: the control diet and the other three enzyme complex supplemented diets which were 180 mg/kg, 360 mg/kg and 720 mg/kg enzyme complex supplemented to the control diet, respectively. The birds fed the diets supplemented with 180 mg/kg and 360 mg/kg enzyme complex had better performance and nutrient availability, the activities of amylase and trypsin in the digestive tract in the two treatments were improved, the villus height and surface area of villus in the small intestine increased and the crypt depth and epithelial thickness of small intestine decreased. Relative weights of pancreas and relative weights and lengths of small intestine decreased. However, the addition of 720 mg/kg enzyme complex had no effects on these parameters and increased crypt depth and epithelial thickness of the small intestine. The data suggested that suitable supplementation of enzyme complex was beneficial for the birds, while excess enzyme complex inhibited secretion of endogenous enzyme and destroyed the structure of the small intestine.

The experiment was conducted to study the effect of choice feeding on growth performance, carcass quality, gastrointestinal development and feed utilization of 22-49 days old broilers. One hundred and forty four 22-day-old broilers were randomly allocated to 3 treatments with 4 replicates per treatment and 12 birds per replicate. Three feeding regimes are complete diet (control), ground corn and protein concentrate (treatment I), and soybean meal and balancer (treatment II). Protein concentrate is the residue part of complete diet without corn, and balancer is the residue part of complete diet without soybean meal. Treatment I and II are designed for the broilers to freely choose the two parts of diet. The results showed that: (1) broilers under choice feeding (treatment I and 11) had lower performances compared with the control; (2) gastrointestinal development and the efficiency ratios that broilers converted dietary crude protein and lysine to body weight gain were improved in treatment I (p 0.05).

Correction for ‘Conformation dynamics of the intrinsically disordered protein c-Myb with the ff99IDPs force field’ by Xiang Guo et al., RSC Adv., 2017, 7, 29713–29721.

Considering a multicast scenario, we want to minimize the coding nodes used for network coding while achieving the desired throughput. By using the genetic and particle swarm algorithm, this article solves the optimization of the network coding. According to the simulation results, it can be concluded that the genetic and particle swarm algorithm has faster convergence speed than the genetic algorithm in solving the problem of network coding optimization, and it can get better suboptimal value in a shorter period of time.

Iron is often found to be of excessive concentrations in laying hens' diets, which may cause antagonistic interactions with other minerals. This study was conducted to investigate how to supplement Zn and Mn in the diets without Fe supplementation. In experiment 1, 420 18-week Lohmann Brown layers were fed a basal diet or a basal diet supplemented with 30-0, 65-30 and 100-60 mg/kg of Zn and Mn, respectively. In experiment 2, 360 40-week Lohmann Brown layers were fed a basal diet or a basal diet supplemented with 15-0, 35-0 and 55-15 mg/kg of Mn and Zn, respectively. Minerals were supplemented in the form of sulfate. Egg production was improved by supplementing 30 mg/kg Zn or 65 mg/kg Zn in combination with 30 mg/kg Mn in experiment one. In experiment two, a significant reduction of egg performance occurred with 35 mg/kg Mn supplementation. Mn and/or Zn supplementation increased eggshell thickness in experiment one, and decreased yolk cholesterol in both experiments. Mn and/or Zn supplementation increased Zn and Mn excretion in both experiments. Serum growth hormone (GH), thyroxine (T(4) ), and insulin levels, or alkaline phosphatase (AP) activity were not affected by treatments; serum estrogen (E(2) ) and triiodothyronine (T(3) ) were different but there was no consistency by dietary treatments. This study demonstrates that 30 mg/kg supplemental Zn is necessary to obtain maximal egg production, and there seems to be no need to supply Mn in this type of diet.